Introduction | Reading expression data from file | Types of expression data | Microarray data | RNA-seq data | Normalization | Differential expression | ID mapping | Enrichment analysis | Obtaining gene sets | Set-based enrichment analysis | Guidelines for input and method selection | Result exploration | Network-based enrichment analysis | User-defined enrichment methods | Combining results | Putting it all together | Advanced: configuration parameters | For non-R users: command line invocation | A primer on terminology and statistical theory | Where does it all come from? | Gene sets, pathways & regulatory networks | Resources | Gene set analysis vs. gene set enrichment analysis | Underlying null: competitive vs. self-contained | Generations: ora, fcs & topology-based | Frequently asked questions | References
Package: EnrichmentBrowser 2.43.0
Ludwig Geistlinger
EnrichmentBrowser: Seamless navigation through combined results of set-based and network-based enrichment analysis
The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.
Authors:
EnrichmentBrowser_2.43.0.tar.gz
EnrichmentBrowser_2.43.0.zip(r-4.7-any)EnrichmentBrowser_2.43.0.zip(r-4.6-any)EnrichmentBrowser_2.43.0.zip(r-4.5-any)
EnrichmentBrowser_2.43.0.tgz(r-4.6-any)EnrichmentBrowser_2.43.0.tgz(r-4.5-any)
EnrichmentBrowser_2.43.0.tar.gz(r-4.7-any)EnrichmentBrowser_2.43.0.tar.gz(r-4.6-any)
EnrichmentBrowser_2.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EnrichmentBrowser/json (API)
| # Install 'EnrichmentBrowser' in R: |
| install.packages('EnrichmentBrowser', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lgeistlinger/enrichmentbrowser/issues
On BioConductor:EnrichmentBrowser-2.43.0(bioc 3.24)EnrichmentBrowser-2.42.0(bioc 3.23)
immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwriting
Last updated from:45eb57e014. Checks:6 ERROR, 2 NOTE, 2 OK. Indexed: yes.
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Exports:combResultscompileGRNconfigEBrowserdeAnadownloadPathwayseaBrowseebrowserexprsHeatmapgetGenesetsggeaGraphggeaGraphLegendgsRankingidMapidTypesimportisAvailablemakeExampleDatanbeanbeaMethodsnormalizepdistrprobe2genereadSEsbeasbeaMethodsshowAvailableCollectionsshowAvailableSpeciesvolcanowriteGMT
Dependencies:abindannotateAnnotationDbiaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiostringsbitbit64bitopsblobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydir.expirydplyredgeRfastmapfilelockgenericsGenomicRangesglueGO.dbgraphgraphiteGSEABasehttrhttr2hwriterIRangesjsonliteKEGGgraphKEGGRESTlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpathviewpillarpkgconfigpngpurrrR6rappdirsRCurlRgraphvizrlangRSQLiteS4ArraysS4VectorssafeSeqinfoSparseArraySparseMSPIAstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXMLxtableXVector
